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Analytical Chemistry Jul 2023Oxidation and protein phosphorylation are critical mechanisms involved in regulating various cellular activities. Increasing research has suggested that oxidative stress...
Oxidation and protein phosphorylation are critical mechanisms involved in regulating various cellular activities. Increasing research has suggested that oxidative stress could affect the activities of specific kinases or phosphatases, leading to alterations in the phosphorylation status of certain proteins. Ultimately, these alterations can affect cellular signaling pathways and gene expression patterns. However, the relationship between oxidation and protein phosphorylation remains complex and not yet fully understood. Therefore, the development of effective sensors capable of detecting both oxidation and protein phosphorylation simultaneously presents an ongoing challenge. To address this need, we introduce a proof-of-concept nanochannel device that is dual-responsive to both HO and phosphorylated peptide (PP). Specifically, we design a peptide GGGCEG(GPGGA)CEGRRRR, which contains an HO-sensitive unit CEG, an elastic peptide fragment (GPGGA), and a phosphorylation site recognition fragment RRRR. When the peptides are immobilized on the inner walls of conical nanochannels in a polyethylene terephthalate membrane, this peptide-modified nanochannel device exhibits a sensitive response to both HO and PPs. The peptide chains undergo a random coil-to-α-helix transition in response to HO, which leads to a close-to-open transition of the nanochannel, accompanied with a remarkable increase in the transmembrane ionic current. In contrast, binding of the peptides with PPs shields the positive charge of the RRRR fragments, causing a decrease of the transmembrane ionic current. These unique features enable the sensitive detection of reactive oxygen species released by 3T3-L1 cells stimulated by platelet-derived growth factor (PDGF) as well as PDGF-induced change in the PP level. Real-time kinase activity monitoring further confirms the device's potential utility for kinase inhibitor screening.
Topics: Hydrogen Peroxide; Peptides; Platelet-Derived Growth Factor; Phosphorylation; Oxidative Stress
PubMed: 37358224
DOI: 10.1021/acs.analchem.3c01458 -
PLoS Computational Biology Feb 2022In-silico methods for the prediction of epitopes can support and improve workflows for vaccine design, antibody production, and disease therapy. So far, the scope of B...
In-silico methods for the prediction of epitopes can support and improve workflows for vaccine design, antibody production, and disease therapy. So far, the scope of B cell and T cell epitope prediction has been directed exclusively towards peptidic antigens. Nevertheless, various non-peptidic molecular classes can be recognized by immune cells. These compounds have not been systematically studied yet, and prediction approaches are lacking. The ability to predict the epitope activity of non-peptidic compounds could have vast implications; for example, for immunogenic risk assessment of the vast number of drugs and other xenobiotics. Here we present the first general attempt to predict the epitope activity of non-peptidic compounds using the Immune Epitope Database (IEDB) as a source for positive samples. The molecules stored in the Chemical Entities of Biological Interest (ChEBI) database were chosen as background samples. The molecules were clustered into eight homogeneous molecular groups, and classifiers were built for each cluster with the aim of separating the epitopes from the background. Different molecular feature encoding schemes and machine learning models were compared against each other. For those models where a high performance could be achieved based on simple decision rules, the molecular features were then further investigated. Additionally, the findings were used to build a web server that allows for the immunogenic investigation of non-peptidic molecules (http://tools-staging.iedb.org/np_epitope_predictor). The prediction quality was tested with samples from independent evaluation datasets, and the implemented method received noteworthy Receiver Operating Characteristic-Area Under Curve (ROC-AUC) values, ranging from 0.69-0.96 depending on the molecule cluster.
Topics: Area Under Curve; Epitopes, B-Lymphocyte; Epitopes, T-Lymphocyte; Peptides; ROC Curve
PubMed: 35180214
DOI: 10.1371/journal.pcbi.1009151 -
Biotechnology Advances 2021Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings,... (Review)
Review
Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings, allowing fast and efficient progress in the field of targeted drug discovery. The identification range comprises low molecular weight peptides up to whole antibodies. However, a major challenge poses the stability and affinity in particular of peptides. Chemical modifications e.g. the introduction of unnatural amino acids or cyclization, have been proven to be essential tools to overcome these limitations. This review article particularly focuses on available methods for the targeted chemical modification of peptides and peptide libraries in selected display approaches.
Topics: Drug Discovery; High-Throughput Screening Assays; Peptide Library; Peptides; Protein Processing, Post-Translational
PubMed: 33513435
DOI: 10.1016/j.biotechadv.2021.107699 -
Electrophoresis Nov 2019Protein SUMOylation modification conjugated with small ubiquitin-like modifiers (SUMOs) is one kind of PTMs, which exerts comprehensive roles in cellular functions,... (Review)
Review
Protein SUMOylation modification conjugated with small ubiquitin-like modifiers (SUMOs) is one kind of PTMs, which exerts comprehensive roles in cellular functions, including gene expression regulation, DNA repair, intracellular transport, stress responses, and tumorigenesis. With the development of the peptide enrichment approaches and MS technology, more than 6000 SUMOylated proteins and about 40 000 SUMO acceptor sites have been identified. In this review, we summarize several popular approaches that have been developed for the identification of SUMOylated proteins in human cells, and further compare their technical advantages and disadvantages. And we also introduce identification approaches of target proteins which are co-modified by both SUMOylation and ubiquitylation. We highlight the emerging trends in the SUMOylation field as well. Especially, the advent of the clustered regularly interspaced short palindromic repeats/ Cas9 technique will facilitate the development of MS for SUMOylation identification.
Topics: CRISPR-Cas Systems; Cells, Cultured; Gene Editing; Humans; Mass Spectrometry; Models, Molecular; Peptides; Recombinant Fusion Proteins; Small Ubiquitin-Related Modifier Proteins; Sumoylation; Ubiquitination
PubMed: 31216068
DOI: 10.1002/elps.201900100 -
Clinical Epigenetics Jul 2019Peptides originating from different sources (endogenous, food derived, environmental, and synthetic) are able to influence different aspects of epigenetic regulation.... (Review)
Review
Peptides originating from different sources (endogenous, food derived, environmental, and synthetic) are able to influence different aspects of epigenetic regulation. Endogenous short peptides, resulting from proteolytic cleavage of proteins or upon translation of non-annotated out of frame transcripts, can block DNA methylation and hereby regulate gene expression. Peptides entering the body by digestion of food-related proteins can modulate DNA methylation and/or histone acetylation while environmental peptides, synthesized by bacteria, fungi, and marine sponges, mainly inhibit histone deacetylation. In addition, synthetic peptides that reverse or inhibit different epigenetic modifications of both histones and the DNA can be developed as well. Next to these DNA and histone modifications, peptides can also influence the expression of non-coding RNAs such as lncRNAs and the maturation of miRNAs.Seen the advantages over small molecules, the development of peptide therapeutics is an interesting approach to treat diseases with a strong epigenetic basis like cancer and Alzheimer's disease. To date, only a limited number of drugs with a proven epigenetic mechanism of action have been approved by the FDA of which two (romidepsin and nesiritide) are peptides. A large knowledge gap concerning epigenetic effects of peptides is present, and this class of molecules deserves more attention in the development as epigenetic modulators. In addition, none of the currently approved peptide drugs are under investigation for their potential effects on epigenetics, hampering drug repositioning of these peptides to other indications with an epigenetic etiology.
Topics: Acetylation; DNA Methylation; Epigenesis, Genetic; Histones; Humans; Peptides
PubMed: 31300053
DOI: 10.1186/s13148-019-0700-7 -
Natural Product Reports May 2024Covering: 2016 to 2023Ribosomally synthesized and posttranslationally modified peptides (RiPPs) continue to be a rich source of chemically diverse and bioactive peptide... (Review)
Review
Covering: 2016 to 2023Ribosomally synthesized and posttranslationally modified peptides (RiPPs) continue to be a rich source of chemically diverse and bioactive peptide natural products. In recent years, cyclophane-containing RiPP natural products and their biosynthetic pathways have been more frequently encountered. This highlight will focus on bacterial monoaryl cyclophane-containing RiPPs. This class of RiPPs is produced by radical SAM/SPASM enzymes that form a crosslink between the aromatic ring and sidechain of two amino acid residues of the precursor peptide. Selected natural products from these pathways exhibit specific antibacterial activity against gram-negative pathogens. The approaches used to discover these pathways and products will be described and categorized as natural product-first or enzyme-first. The breadth of ring systems formed by the enzymes, enzyme mechanism, and recent reports of synthetic methods for constructing these ring systems will also be presented. Bacterial cyclophane-containing RiPPs and their biosynthetic enzymes represent an untapped source of scaffolds for drug discovery and tools for synthetic biology.
Topics: Biological Products; Protein Processing, Post-Translational; Molecular Structure; Anti-Bacterial Agents; Bacteria; S-Adenosylmethionine; Peptides; Bacterial Proteins; Biosynthetic Pathways; Cyclophanes
PubMed: 38047390
DOI: 10.1039/d3np00030c -
International Journal of Molecular... May 2023Enteroendocrine cells are specialized secretory lineage cells in the small and large intestines that secrete hormones and peptides in response to luminal contents. The... (Review)
Review
Enteroendocrine cells are specialized secretory lineage cells in the small and large intestines that secrete hormones and peptides in response to luminal contents. The various hormones and peptides can act upon neighboring cells and as part of the endocrine system, circulate systemically via immune cells and the enteric nervous system. Locally, enteroendocrine cells have a major role in gastrointestinal motility, nutrient sensing, and glucose metabolism. Targeting the intestinal enteroendocrine cells or mimicking hormone secretion has been an important field of study in obesity and other metabolic diseases. Studies on the importance of these cells in inflammatory and auto-immune diseases have only recently been reported. The rapid global increase in metabolic and inflammatory diseases suggests that increased understanding and novel therapies are needed. This review will focus on the association between enteroendocrine changes and metabolic and inflammatory disease progression and conclude with the future of enteroendocrine cells as potential druggable targets.
Topics: Intestines; Enteroendocrine Cells; Biological Transport; Peptides; Hormones
PubMed: 37240181
DOI: 10.3390/ijms24108836 -
Cell Chemical Biology Jul 2023Inhibition of protein-protein interactions (PPIs) via designed peptides is an effective strategy to perturb their biological functions. The Elongin BC heterodimer...
Inhibition of protein-protein interactions (PPIs) via designed peptides is an effective strategy to perturb their biological functions. The Elongin BC heterodimer (ELOB/C) binds to a BC-box motif and is essential for cancer cell growth. Here, we report a peptide that mimics the high-affinity BC-box of the PRC2-associated protein EPOP. This peptide tightly binds to the ELOB/C dimer (k = 0.46 ± 0.02 nM) and blocks the association of ELOB/C with its interaction partners, both in vitro and in the cellular environment. Cancer cells treated with our peptide inhibitor showed decreased cell viability, increased apoptosis, and perturbed gene expression. Therefore, our work proposes that blocking the BC-box-binding pocket of ELOB/C is a feasible strategy to impair its function and inhibit cancer cell growth. Our peptide inhibitor promises novel mechanistic insights into the biological function of the ELOB/C dimer and offers a starting point for therapeutics linked to ELOB/C dysfunction.
Topics: Elongin; Transcription Factors; Protein Binding; Peptides; Apoptosis; Ubiquitin-Protein Ligases; Neoplasms
PubMed: 37354906
DOI: 10.1016/j.chembiol.2023.05.012 -
Biochemical Pharmacology Nov 2023GPR81, initially discovered in adipocytes, has been found to suppress lipolysis when activated. However, the current small molecules that target GPR81 carry the risk of...
GPR81, initially discovered in adipocytes, has been found to suppress lipolysis when activated. However, the current small molecules that target GPR81 carry the risk of off-target effects, and their impact on tumor progression remains uncertain. Here, we utilized phage display technology to screen a GPR81-targeting peptide named 7w-2 and proceeded to demonstrate its bioactivity. Although 7w-2 did not affect the proliferation of tumor cells, it effectively reduced adipocyte catabolism in vitro, consequently restraining the proliferation of co-cultured tumor cells. Furthermore, our findings revealed that 7w-2 could inhibit lipolysis in vivo, leading to a significant impediment in tumor growth and metastasis in the 4T1 murine tumor model. Additionally, 7w-2 exhibited the ability to significantly elevate the proportion and functionality of CD8 T cells. Our study introduces 7w-2 as the first peptide targeting GPR81, shedding light on its potential role in adipocytes in suppressing tumor progression.
Topics: Mice; Animals; Receptors, G-Protein-Coupled; CD8-Positive T-Lymphocytes; Adipocytes; Lipolysis; Peptides
PubMed: 37696459
DOI: 10.1016/j.bcp.2023.115800 -
Current Opinion in Pharmacology Jun 2023Peptides form the largest group of ligands that modulate the activity of more than 120 different GPCRs. Among which linear disordered peptide ligands usually undergo... (Review)
Review
Peptides form the largest group of ligands that modulate the activity of more than 120 different GPCRs. Among which linear disordered peptide ligands usually undergo significant conformational changes upon binding that is essential for receptor recognition and activation. Conformational selection and induced fit are the extreme mechanisms of coupled folding and binding that can be distinguished by analysis of binding pathways by methods that include NMR. However, the large size of GPCRs in membrane-mimetic environments limits NMR applications. In this review, we highlight advances in the field that can be adopted to address coupled folding and binding of peptide ligands to their cognate receptors.
Topics: Humans; Receptors, G-Protein-Coupled; Ligands; Peptides; Protein Binding
PubMed: 37003111
DOI: 10.1016/j.coph.2023.102366